Molecular dynamics simulation features

In literature, some researchers regarded that the continuum mechanic ceases to be valid to describe the lubrication behavior when clearance decreases down to such a limit. Reasons cited for the inadequacy of continuum methods applied to the lubrication confined between two solid walls in relative motion are that the problem is so complex that any theoretical approach is doomed to failure, and that the film is so thin, being inherently of molecular scale, that modeling the material as a continuum ceases to be valid. Due to the molecular orientation, the lubricant has an underlying microstructure. They turned to molecular dynamic simulation for help, from which macroscopic flow equations are drawn. This is also validated through molecular dynamic simulation by Hu et al. [6,7] and Mark et al. [8]. To date, experimental research had "got a little too far forward on its skis however, theoretical approaches have not had such rosy prospects as the experimental ones have. Theoretical modeling of the lubrication features associated with TFL is then urgently necessary. 

Many molecular dynamics simulations have focused on the electrolyte solution factors and ignored the atomic features of the pore wall. The assumptions of these simulations may match more closely the experiments of inorganic channels, such as track-etched nu-... 

A detailed study of the mechanism of the enantioselective palladium catalyzed hydrosilylation of styrene with trichlorosilane was carried out with combined QM/MM ab initio molecular dynamics simulations. A number of fundamental mechanistic questions have been addressed, including the main features of the catalytic cycle, as well as the specific nature of the regioselectivity and enatioselectivity. 

Lippa, K.A., Sander, L.C., and Mountain, R.D., Identification of isolated cavity features within molecular dynamics simulated chromatographic surfaces, J. Chromatogr. A, 1128, 79, 2006. 

The above discussion was based on the results of molecular dynamics simulations on unsaturated or conjugated hydrocarbons. Although the general features can be extended to molecular structures of more general types, in practice it is appropriate to consider the specific form of the electron orbitals involved. For instance, d d transitions in transition metal ion complexes involve orbitals mainly localized on the metal ion that, in the crystal field... 

A fully deuterated powder of the photosynthetic protein C-phycocyanin (CPC) has been investigated by NSE in a similar (Q,t)-range [335]. Here the coherent scattering conveying the pair correlation Spair(Q,t)/SpaiAQ) in terms of the intermediate scattering function was obtained and compared to molecular dynamics simulations. As illustrated in Fig. 6.31 the salient features of the NSE data were quantitatively and qualitatively reproduced by the MD results [348]. 

Of great interest to the molecular biologist is the relationship of protein form to function. Recent years have shown that although structural information is necessary, some appreciation of the molecular flexibility and dynamics is essential. Classically this information has been derived from the crystallographic atomic thermal parameters and more recently from molecular dynamics simulations (see for example McCammon 1984) which yield independent atomic trajectories. A diaracteristic feature of protein crystals, however, is that their diffraction patterns extend to quite limited resolution even employing SR. This lack of resolution is especially apparent in medium to large proteins where diffraction data may extend to only 2 A or worse, thus limiting any analysis of the protein conformational flexibility from refined atomic thermal parameters. It is precisely these crystals where flexibility is likely to be important in the protein function. 

The most striking feature of AIMD and the novelty over traditional molecular dynamics simulations is the fact that the electronic structure is available all the time. Therefore, the analysis of the wavefunction in the course of the simulation or along the trajectory is one of the major subjects that can contribute to the understanding on the molecular and on the electronic level. The importance of analyzing the wavefunction in bioinorganic systems has been shown in many applications, see also Section... 

In the applications of the PCM approach to SD, the focus so far has been mainly on the comparison with experiment [45,46] and very good agreement with experimental results has been obtained for C153 in several polar liquids [45], In the case of SD in water, the theory was implemented using two different approaches to obtain e(w), either a fit to experimental data [45] or a calculation of the dipole density time correlation from molecular dynamics simulation [46], While the results for S(t) that use experimental dielectric permittivity as input look quite similar to those shown in Figure 3.16, the results based on the simulation data exhibit more pronounced oscillatory features at the characteristic frequency of the hydrogen bond librations. 

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